X-Men Origins: Wolverine was just saddled with problems. It went over-budget, over-schedule, and director Gavin Hood (who had no prior experience directing a big-budget movie) butted heads with 20th Century Fox exec Tom Rothman a lot during filming. For example, Hood would give direction, and then allegedly Rothman would circumvent Hood, creating problems on set.

According to rumors, Richard Donner (director of Superman: The Movie and husband of producer Lauren Shuler-Donner, who produces all the X-Men films) was called in to direct a pivotal action sequence because Hood apparently lacked the proper experience to do that sequence justice. I'm not sure if that's true or not, but that's what I heard.

EDIT: From Wikipedia, which is admittedly not the most reliable of sources, but I've heard this story in other places before.

Hood and Fox were in dispute on the film's direction. One of the disputes involved the depiction of Wolverine as an Army veteran with post-traumatic stress disorder, with the executives arguing that audiences would not be interested in such heavy themes. The studio had two replacements lined up before Richard Donner, husband of producer Lauren Shuler Donner, flew to Australia to ease on-set tensions. Hood remarked, "Out of healthy and sometimes very rigorous debate, things get better. [...] I hope the film's better because of the debates. If nobody were talking about us, we'd be in trouble!" Hood added he and Thomas Rothman were both "forceful" personalities in creative meetings but they had never had a "stand-up" argument.

Gavin Hood is a very good director as has been stated before. Hood's films Tsotsi and Rendition received good reviews. However, not every director can seamlessly transition to mainstream films. I think in order to do that you need a supportive studio backing you and 20th Century Fox is known for meddling in affairs of other filmmakers. Bryan Singer had a very difficult time making the first two X-Men movies which is why he left X-Men: The Last Stand to direct Superman Returns. However, I think after the poor reception to both X-Men: The Last Stand and X-Men Origins: Wolverine, Fox and Rothman realized their mistakes and have since changed their ways. Or so I hope.